dbSNP rs1511024: FABP2:c.*15G>A (chr4-119319026-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000134.4(FABP2):c.*15G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 1,585,764 control chromosomes in the GnomAD database, including 1,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.041 ( 193 hom., cov: 32)

Exomes 𝑓: 0.033 ( 920 hom. )

Consequence

FABP2
NM_000134.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.286

Publications

9 publications found

Variant links:

Genes affected

FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

FABP2 links:

ENSG00000294020 (HGNC:):

ENSG00000294020 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 4-119319026-C-T is Benign according to our data. Variant chr4-119319026-C-T is described in ClinVar as Benign. ClinVar VariationId is 1226479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	NM_000134.4	MANE Select	c.*15G>A		3_prime_UTR	Exon 4 of 4	NP_000125.2	P12104

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FABP2	ENST00000274024.4	TSL:1 MANE Select	c.*15G>A	3_prime_UTR	Exon 4 of 4	ENSP00000274024.3	P12104
ENSG00000294020	ENST00000720595.1		n.176-15302C>T	intron	N/A
ENSG00000294020	ENST00000720596.1		n.224-15302C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0414

AC:

6292

AN:

151858

Hom.:

191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0642

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.0341

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.00578

Gnomad SAS

AF:

0.0321

Gnomad FIN

AF:

0.0373

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0340

Gnomad OTH

AF:

0.0418

GnomAD2 exomes

AF:

0.0325

AC:

7602

AN:

234116

AF XY:

0.0330

show subpopulations

Gnomad AFR exome

AF:

0.0629

Gnomad AMR exome

AF:

0.0185

Gnomad ASJ exome

AF:

0.0164

Gnomad EAS exome

AF:

0.00569

Gnomad FIN exome

AF:

0.0377

Gnomad NFE exome

AF:

0.0352

Gnomad OTH exome

AF:

0.0385

GnomAD4 exome

AF:

0.0329

AC:

47174

AN:

1433788

Hom.:

920

Cov.:

AF XY:

0.0330

AC XY:

23580

AN XY:

714010

show subpopulations

African (AFR)

AF:

0.0584

AC:

1849

AN:

31654

American (AMR)

AF:

0.0212

AC:

864

AN:

40736

Ashkenazi Jewish (ASJ)

AF:

0.0168

AC:

432

AN:

25770

East Asian (EAS)

AF:

0.0147

AC:

557

AN:

37788

South Asian (SAS)

AF:

0.0372

AC:

3099

AN:

83324

European-Finnish (FIN)

AF:

0.0388

AC:

2062

AN:

53128

Middle Eastern (MID)

AF:

0.104

AC:

587

AN:

5658

European-Non Finnish (NFE)

AF:

0.0325

AC:

35659

AN:

1096554

Other (OTH)

AF:

0.0349

AC:

2065

AN:

59176

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.419

Heterozygous variant carriers

1875

3750

5626

7501

9376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1296

2592

3888

5184

6480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0415

AC:

6301

AN:

151976

Hom.:

193

Cov.:

AF XY:

0.0418

AC XY:

3106

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.0641

AC:

2662

AN:

41498

American (AMR)

AF:

0.0339

AC:

517

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.0159

AC:

AN:

3462

East Asian (EAS)

AF:

0.00580

AC:

AN:

5176

South Asian (SAS)

AF:

0.0322

AC:

155

AN:

4818

European-Finnish (FIN)

AF:

0.0373

AC:

393

AN:

10548

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0340

AC:

2309

AN:

67918

Other (OTH)

AF:

0.0447

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

317

635

952

1270

1587

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0407

Hom.:

Bravo

AF:

0.0411

Asia WGS

AF:

0.0360

AC:

124

AN:

3458

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.1

(source)

DANN

Benign

0.62

PhyloP100

-0.29

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over